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Author SHA1 Message Date
Dannon Baker f576258320 Move global type declarations to types dir 2022-12-05 08:59:41 -05:00
Dannon Baker b8fa41a285 Explicitly include vue type shim. It's always the small things... 2022-12-05 08:59:41 -05:00
Dannon Baker 7eca34139c Add vue shim 2022-12-05 08:59:41 -05:00
Dannon Baker 5521dc79a4 Allow synthetic default imports 2022-12-05 08:59:41 -05:00
Dannon Baker de0c6e8afb Set up eslint correctly for typescript 2022-12-05 08:59:41 -05:00
Dannon Baker 3ed7e29350 Updates to tsconfig; scope include correctly and use es2015 modules instead of cjs. 
Upgrade typescript/ts-loader
 2022-12-05 08:59:41 -05:00
Dannon Baker 96ce630d2b incremental work, it compiles? 2022-12-05 08:59:41 -05:00
Dannon Baker f83c10bffb Initial deps and config for typescript 2022-12-05 08:59:41 -05:00
Dannon 6b764f3897 Merge pull request #15103 from galaxyproject/dependabot/npm_and_yarn/client/decode-uri-component-0.2.1 
Bump decode-uri-component from 0.2.0 to 0.2.1 in /client
 2022-12-04 07:38:36 -05:00
Nicola Soranzo 69e4e4e7d9 Merge pull request #15104 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2022-12-03 22:16:06 +00:00
galaxybot bbd0e64474 Update Python dependencies 2022-12-03 16:32:25 +00:00
Aysam Guerler 4c40fe8071 Merge pull request #15082 from guerler/composition_bar 
Use Galaxy logo instead of Logo/Text combo, refactor masthead to composition api
 2022-12-03 10:41:09 -05:00
Björn Grüning 6a5608bcd6 Merge pull request #15031 from jmchilton/structured_test_decorators 
Infrastructure for indicating Galaxy features being used by tests.
 2022-12-03 10:34:49 +01:00
dependabot[bot] 0dca4db440 Bump decode-uri-component from 0.2.0 to 0.2.1 in /client 
Bumps [decode-uri-component](https://github.com/SamVerschueren/decode-uri-component) from 0.2.0 to 0.2.1.
- [Release notes](https://github.com/SamVerschueren/decode-uri-component/releases)
- [Commits](https://github.com/SamVerschueren/decode-uri-component/compare/v0.2.0...v0.2.1)

---
updated-dependencies:
- dependency-name: decode-uri-component
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
 2022-12-02 16:44:00 +00:00
Dannon b3f0098ddb Merge pull request #15102 from nsoranzo/js_lint_github_wf 
Move JavaScript linting to GitHub workflows
 2022-12-02 11:43:24 -05:00
Nicola Soranzo 71be0f9743 Move JavaScript linting to GitHub workflows 2022-12-02 15:09:31 +00:00
Marius van den Beek 0fa38eebec Merge pull request #15094 from davelopez/fix_short_term_storage_api 
Various fixes for Short Term Storage API
 2022-12-02 11:12:34 +01:00
davelopez a8dd40e0ab Fix typing in test populator 2022-12-02 09:57:29 +01:00
davelopez f98da7349c Fix UUID serialization in Celery 
Most objects at `lib/galaxy/web/short_term_storage/__init__.py` are declared as `dataclass` (and not Pydantic models), so the UUID won't be automatically serialized.
 2022-12-02 09:57:29 +01:00
davelopez 99166d0863 Make short_term_storage_request_id an UUID instead of str 
This provides correct typing and validation directly in the API
 2022-12-02 09:57:29 +01:00
davelopez efcf76e3b5 Return 404 when target expires or doesn't exists 2022-12-02 09:57:29 +01:00
David López fbf076c0ce Merge pull request #15099 from davelopez/fix_flaky_api_test 
Sort library folders by name by default
 2022-12-01 22:13:01 +01:00
davelopezandNicola Soranzo 4566b59c01 Make sure there is no ambiguity ordering by type 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2022-12-01 19:11:02 +01:00
davelopez 464368ebf3 Sort always folders by name 
If the folder cannot be sorted by the specified column
 2022-12-01 18:48:11 +01:00
John Davis 0aa0feb610 Merge pull request #15004 from jdavcs/dev_mypy_workflow 
Run mypy on a fully loaded galaxy venv for stricter type checking
 2022-11-30 22:30:37 -05:00
John Davis f07207ad6d Use 3 requirements files in the key for pip cache 2022-11-30 21:10:04 -05:00
Nicola Soranzo 303f1a04af Revert "Add type annotation to `config attribute of MinimalToolApp` protocol" 
This reverts commit b1c35bfc6a.

Also, add comment about why `MinimalToolApp.config` should be type annotated as `Any`.
 2022-12-01 01:52:25 +00:00
Dannon 4c7018caba Merge pull request #15095 from nsoranzo/test_pkce 
Add ``pkce`` to dev/test requirements
 2022-11-30 19:42:54 -05:00
guerler 91455ce2d2 Remove project from logo 2022-11-30 17:19:07 -05:00
guerler 2d7414116b Remove debug statement 2022-11-30 17:19:07 -05:00
guerler 60c50784fc Adjust jest tests to refactored components 2022-11-30 17:19:07 -05:00
guerler 996374c4b8 Remove unused import, avoid undefined class 2022-11-30 17:19:07 -05:00
guerler b7bf01a212 Fix alignment, replace hover title to indicate actual action 2022-11-30 17:19:07 -05:00
guerler 72fd52f087 Deprecate brand title text option, logo now contains text 2022-11-30 17:19:07 -05:00
guerler 95dadf3491 Rewrite masthead as composition, replace logo/text with logo only 2022-11-30 17:19:07 -05:00
Martin Cech 22682a9795 Merge pull request #15096 from abueg/patch-1 
Fix broken `resubmission_job_conf.xml` reference in documentation
 2022-11-30 21:02:04 +01:00
Linelle 9c5f5bc3a2 changed references from sample XML to sample YML 
added a sentence about where to find the XMLs as well in case people are still using those (it's me, i'm people)
 2022-11-30 14:50:19 -05:00
John Davis b8f2aec155 Combine update lint/typecheck reqs scripts 2022-11-30 14:44:30 -05:00
Linelle ec504562e3 change resubmission example link from xml to yml 
Test case for resubmission location used to be https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.xml which leads to 404, have changed it to https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.yml and made it linked text instead of plain URL
 2022-11-30 14:29:52 -05:00
Martin Cech 0b53cf510a Merge pull request #13815 from bernt-matthias/topic/expect_test_failure 
expect_test_failure: also test if no failure was found
 2022-11-30 20:14:50 +01:00
Martin Cech 35e1ec5bd1 Merge pull request #14914 from ElectronicBlueberry/mark-optional-followup 
Mark optional form parameters followup
 2022-11-30 20:11:23 +01:00
Martin Cech e4becc21a0 Merge pull request #14959 from bernt-matthias/topic/lint-expect_failure_num_outputs 
lint for coexisting expect_num_outputs and expect_failure
 2022-11-30 20:06:29 +01:00
John Davis 578fe8ae98 Revert "Add new target to Makefile" 
This reverts commit 9f42c7b71a.
 2022-11-30 13:41:16 -05:00
John DavisandNicola Soranzo 02ea4f531e Drop unused attr 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 13:39:16 -05:00
John DavisandNicola Soranzo 67c7e7d1ac Use a simple cast instead of relying on dependency injection 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 13:33:42 -05:00
Nicola Soranzo b1c35bfc6a Add type annotation to `config attribute of MinimalToolApp` protocol 2022-11-30 17:57:29 +00:00
Nicola Soranzo 139d14e952 Fix `object_store type in MinimalToolApp` protocol 2022-11-30 17:55:04 +00:00
Nicola Soranzo 3d5bcff5c1 Add pkce to dev/test requirements 
So `test_authenticate_set_pkce_verifier_cookie` unit test is not skipped.
 2022-11-30 16:34:32 +00:00
John DavisandNicola Soranzo 786a3e4375 Don't pip-install lint requirements for package tests 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 11:31:22 -05:00
John DavisandNicola Soranzo 1d75a584d6 Keep cache key suffix same as workflow filename 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 11:27:41 -05:00